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Background:Long-standing ulcerative colitis (UC) leading to colorectal cancer (CRC) is one of the most serious and life-threatening consequences acknowledged globally. Ulcerative colitis-associated colorectal carcinogenesis showed distinct molecular alterations when compared with sporadic colorectal carcinoma.Methods:Targeted sequencing of 409 genes in tissue samples of 18 long-standing UC subjects at high risk of colorectal carcinoma (UCHR) was performed to identify somatic driver mutations, which may be involved in the molecular changes during the transformation of non-dysplastic mucosa to high-grade dysplasia. Findings from the study are also compared with previously published genome wide and exome sequencing data in inflammatory bowel disease-associated and sporadic colorectal carcinoma.Results:Next-generation sequencing analysis identified 1107 mutations in 275 genes in UCHR subjects. In addition to TP53 (17%) and KRAS (22%) mutations, recurrent mutations in APC (33%), ACVR2A (61%), ARID1A (44%), RAF1 (39%) and MTOR (61%) were observed in UCHR subjects. In addition, APC, FGFR3, FGFR2 and PIK3CA driver mutations were identified in UCHR subjects. Recurrent mutations in ARID1A (44%), SMARCA4 (17%), MLL2 (44%), MLL3 (67%), SETD2 (17%) and TET2 (50%) genes involved in histone modification and chromatin remodelling were identified in UCHR subjects.Conclusions:Our study identifies new oncogenic driver mutations which may be involved in the transition of non-dysplastic cells to dysplastic phenotype in the subjects with long-standing UC with high risk of progression into colorectal neoplasia.

Three hundred and three chicks of both sexes, from a synthetic dam line (SDL) of broiler chickens, were studied for economic traits (body weights at 4, 5 and 6 weeks of age) and immunological traits (humoral and cell mediated immune responses, and serum lysozyme concentration). The objective was to evaluate these traits and to estimate their genetic and non-genetic parameters. The humoral immune response was assessed by estimating the antibody response to sheep red blood cells using the haemagglutination (HA) test and serum IgG concentration using single radial immunodiffusion (SRID). The cell mediated immune (CMI) response was estimated as in vivo response to a mitogen (PHA-P). Serum lysozyme was measured by lysoplate assay. Least squares means for body weight at 4, 5 and 6 weeks were 684 +/- 20, 920 +/- 19 and 1205 +/- 28 g, HA titre was 6.289 +/- 0.246, CMI was 0.438 +/- 0.015 mm, lysozyme was 1.860 +/- 0.047 microg/ml and IgG was 6.287 +/- 0.194 mg/ml. There was an effect of sire on HA titre and on body weight at 4, 5 and 6 weeks of age; males were heavier than females. Heritability estimates were high for body weights but low for immunological traits. Phenotypic correlations (rp) among body weights were high and positive but were very low between body weights and most immunological traits. Among the immunological traits all rp were very low. Genetic correlations (rg) of body weights were positive and medium to high with CMI and HA and negative with serum IgG.

BackgroundThe incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection. Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the copy number variations (CNVs) and the associated genes which could be potential markers for the detection of neoplasia in both ulcerative colitis-associated neoplasia (UC-CRN) and sporadic colorectal neoplasia (S-CRN).MethodsWe employed array comparative genome hybridization (aCGH) to identify CNVs in tissue samples of UC nonprogressor, progressor and sporadic CRC. Select genes within these CNV regions as a panel of markers were validated using quantitative real time PCR (qRT-PCR) method along with the microsatellite instability (MSI) in an independent cohort of samples. Immunohistochemistry (IHC) analysis was also performed.ResultsIntegrated analysis showed 10 overlapping CNV regions between UC-Progressor and S-CRN, with the 8q and 12p regions showing greater overlap. The qRT-PCR based panel of MYC, MYCN, CCND1, CCND2, EGFR and FNDC3A was successful in detecting neoplasia with an overall accuracy of 54 % in S-CRN compared to that of 29 % in UC neoplastic samples. IHC study showed that p53 and CCND1 were significantly overexpressed with an increasing frequency from pre-neoplastic to neoplastic stages. EGFR and AMACR were expressed only in the neoplastic conditions.ConclusionCNVs that are common and unique to both UC-associated and sporadic colorectal neoplasm could be the key players driving carcinogenesis. Comparative analysis of CNVs provides testable driver aberrations but needs further evaluation in larger cohorts of samples. These markers may help in developing more effective neoplasia-detection strategies during screening and surveillance programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-016-2303-4) contains supplementary material, which is available to authorized users.

Increasing numbers of CNVs are associated with the progression of UC to CAC, and warrant further detailed exploration.

High-grade dysplasia and subsequent adenocarcinoma can be detected with careful follow-up in Indian patients with long-standing UC but acceptance of surveillance and subsequent therapy are suboptimal. We found evidence that screening and surveillance programmes are useful for detecting neoplasias in UC, and need to be customized for this region.

Energy undernutrition occurs equally commonly in TP and ACP and this appears to develop after the onset of illness.